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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ), 'gf_id' => 'HOM05D001486', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001486' ), 'data_identifier' => 'HOM05D001486', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001486', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p32260' => 'bna', 'A06p10890' => 'bna', 'A06p44170' => 'bna', 'A09p23570' => 'bna', 'A09p61750' => 'bna', 'Aa31LG1G250' => 'aar', 'Aa31LG1G260' => 'aar', 'Aa31LG2G8200' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2159' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2276' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1455' => 'aag', 'Actinidia12394' => 'ach', 'Actinidia34036' => 'ach', 'Actinidia36627' => 'ach', 'Actinidia38441' => 'ach', 'Ah.03g137420' => 'amhyb', 'Ah.13g072990' => 'amhyb', 'AL1G26870' => 'aly', 'AL1G32070' => 'aly', 'AL1G32080' => 'aly', 'AL2G18360' => 'aly', 'AL3G34910' => 'aly', 'AL3G34920' => 'aly', 'AL5G10790' => 'aly', 'Aqoxy3G00010' => 'aox', 'Aqoxy3G03310' => 'aox', 'Aqoxy7G03241' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56F275' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK3VI9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G5DQ32' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JC79MH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WZE3XK' => 'arhy', 'AT1G14850' => 'ath', 'AT2G01690' => 'ath', 'ATR0753G082' => 'atr', 'ATR0753G157' => 'atr', 'Atru.chr11.925' => 'acertr', 'Atru.chr11.926' => 'acertr', 'AUR62002589' => 'cqu', 'AUR62014245' => 'cqu', 'AUR62030013' => 'cqu', 'AUR62038470' => 'cqu', 'BcaB02g06554' => 'bca', 'BcaB07g30379' => 'bca', 'BcaB07g30727' => 'bca', 'BcaB08g34420' => 'bca', 'BcaC01g04114' => 'bca', 'BcaC03g17068' => 'bca', 'BcaC04g21555' => 'bca', 'BcaC04g21556' => 'bca', 'BcaC05g25406' => 'bca', 'BcaC06g31283' => 'bca', 'BcaC06g34133' => 'bca', 'BcaC07g41534' => 'bca', 'BcaC09g49263' => 'bca', 'BolC2t11065H' => 'bol', 'BolC5t30028H' => 'bol', 'BolC5t30030H' => 'bol', 'BolC7t43769H' => 'bol', 'BolC7t43882H' => 'bol', 'BolC8t52091H' => 'bol', 'BolC9t55904H' => 'bol', 'BraA02t08243Z' => 'bra', 'BraA06t24267Z' => 'bra', 'BraA06t27292Z' => 'bra', 'BraA09t37961Z' => 'bra', 'BraA09t41545Z' => 'bra', 'C02p49860' => 'bna', 'C05p12830' => 'bna', 'C07p32330' => 'bna', 'C08p45360' => 'bna', 'C09p30410' => 'bna', 'CAN.G149.16' => 'can', 'CAN.G3126.1' => 'can', 'CAN.G406.6' => 'can', 'CAN.G601.1' => 'can', 'CAN.G601.2' => 'can', 'CAN.G74.5' => 'can', 'CANSAT01G0610' => 'cansat', 'CANSAT01G1659' => 'cansat', 'CARHR015390' => 'chi', 'CARHR144260' => 'chi', 'CARHR227050' => 'chi', 'CARHR267550' => 'chi', 'Carub.0001s1464' => 'cru', 'Carub.0005s0064' => 'cru', 'Carub.0127s0003' => 'cru', 'Ca_12547_v3' => 'car', 'Ca_17256_v3' => 'car', 'Ca_17277_v3' => 'car', 'Ca_17278_v3' => 'car', 'CBR_g22971' => 'cbr', 'Cc04_g10510' => 'ccan', 'Cc11_g07260' => 'ccan', 'Cc11_g07270' => 'ccan', 'CDE04G1077' => 'cde', 'CDE04G2443' => 'cde', 'CDE06G1153' => 'cde', 'CDE06G1861' => 'cde', 'CDE06G2592' => 'cde', 'CDE07G0203' => 'cde', 'CDE07G1854' => 'cde', 'Cfa012913' => 'cfa', 'Cfa015023' => 'cfa', 'Cfa024922' => 'cfa', 'Ciclev10014036m.g' => 'ccl', 'Ciclev10014409m.g' => 'ccl', 'CiPaw.05G189200' => 'cil', 'CiPaw.06G051700' => 'cil', 'CiPaw.06G051900' => 'cil', 'ClCG01G015310' => 'cla', 'ClCG07G005610' => 'cla', 'ClCG07G005650' => 'cla', 'COL.COLO4_16586' => 'col', 'COL.COLO4_16587' => 'col', 'COL.COLO4_16588' => 'col', 'Cpa.g.sc2.194' => 'cpa', 'Cpa.g.sc2.195' => 'cpa', 'Cre09.g394350' => 'cre', 'Cre16.g670261' => 'cre', 'CsaV3_5G015740' => 'csa', 'CsaV3_5G036990' => 'csa', 'CSS0002688' => 'camsi', 'CSS0012816' => 'camsi', 'CSS0022032' => 'camsi', 'CSS0024241' => 'camsi', 'CSS0030809' => 'camsi', 'CSS0033625' => 'camsi', 'CSS0037038' => 'camsi', 'CSS0044357' => 'camsi', 'CSS0045072' => 'camsi', 'DCAR_005364' => 'dca', 'DCAR_007328' => 'dca', 'DCAR_007329' => 'dca', 'DCAR_030270' => 'dca', 'Dinv07730' => 'din', 'Dinv07731' => 'din', 'Dinv08623' => 'din', 'Dinv08676' => 'din', 'Dinv09695' => 'din', 'Dinv10475' => 'din', 'Dinv10476' => 'din', 'Dinv16909' => 'din', 'Dinv34965' => 'din', 'Dinv40940' => 'din', 'Duzib248G0925' => 'dzi', 'Duzib251G0538' => 'dzi', 'Duzib251G0612' => 'dzi', 'Duzib268G0262' => 'dzi', 'Duzib268G0355' => 'dzi', 'ECA233G0786' => 'eca', 'ECA233G3229' => 'eca', 'ECA246G1671' => 'eca', 'ECA246G3923' => 'eca', 'ECA247G0951' => 'eca', 'EL10Ac3g06288' => 'bvu', 'EL10Ac6g14120' => 'bvu', 'Eucgr.G02106' => 'egr', 'Eucgr.G02107' => 'egr', 'FAN07G1595' => 'fan', 'FAN12G0503' => 'fan', 'FAN12G1020' => 'fan', 'FAN17G1739' => 'fan', 'FAN17G1742' => 'fan', 'FAN22G2360' => 'fan', 'FAN22G2372' => 'fan', 'FvH4_1g18130' => 'fve', 'FvH4_4g33560' => 'fve', 'FvH4_4g33570' => 'fve', 'Glyma.02G085000' => 'gma', 'Glyma.05G238700' => 'gma', 'Glyma.05G238800' => 'gma', 'Glyma.07G169700' => 'gma', 'Glyma.08G045800' => 'gma', 'Glyma.08G045900' => 'gma', 'Gohir.A01G147000' => 'ghi', 'Gohir.A03G115400' => 'ghi', 'Gohir.A04G142700' => 'ghi', 'Gohir.A05G308900' => 'ghi', 'Gohir.A12G152100' => 'ghi', 'Gohir.D01G140100' => 'ghi', 'Gohir.D02G139700' => 'ghi', 'Gohir.D04G186000' => 'ghi', 'Gohir.D05G309600' => 'ghi', 'Gorai.002G172300' => 'gra', 'Gorai.005G157100' => 'gra', 'Gorai.008G168200' => 'gra', 'Gorai.009G330200' => 'gra', 'Gorai.012G182400' => 'gra', 'GSVIVG01000371001' => 'vvi', 'GSVIVG01001572001' => 'vvi', 'GSVIVG01011661001' => 'vvi', 'GSVIVG01011662001' => 'vvi', 'GSVIVG01011664001' => 'vvi', 'GSVIVG01026805001' => 'vvi', 'GSVIVG01029397001' => 'vvi', 'HanXRQChr01g0015621' => 'han', 'HanXRQChr08g0212491' => 'han', 'HanXRQChr08g0212501' => 'han', 'HanXRQChr12g0363231' => 'han', 'HanXRQChr12g0371181' => 'han', 'HanXRQChr14g0441031' => 'han', 'HanXRQChr15g0476741' => 'han', 'HanXRQChr17g0566591' => 'han', 'HanXRQChr17g0566601' => 'han', 'HanXRQChr17g0567281' => 'han', 'Haze_10881' => 'cav', 'Haze_10882' => 'cav', 'Haze_26306' => 'cav', 'Hma1.2p1_0053F.1_g030840' => 'hma', 'Hma1.2p1_0277F.1_g111730' => 'hma', 'Hma1.2p1_0277F.1_g111740' => 'hma', 'Hma1.2p1_0705F.1_g206905' => 'hma', 'Hma1.2p1_0705F.1_g206910' => 'hma', 'Hma1.2p1_0705F.1_g206960' => 'hma', 'Hma1.2p1_0940F.1_g239570' => 'hma', 'Hma1.2p1_0940F.1_g239580' => 'hma', 'Hma1.2p1_0940F.1_g239590' => 'hma', 'Hma1.2p1_0940F.1_g239595' => 'hma', 'HPP92_002282' => 'vpl', 'HPP92_020315' => 'vpl', 'HPP92_024794' => 'vpl', 'HPP92_024797' => 'vpl', 'HPP92_024812' => 'vpl', 'Hund13366' => 'sun', 'Hund20674' => 'sun', 'Hund20676' => 'sun', 'Hund24926' => 'sun', 'Lalb_Chr04g0258641' => 'lal', 'Lalb_Chr05g0222211' => 'lal', 'Lalb_Chr09g0330891' => 'lal', 'Lalb_Chr09g0330901' => 'lal', 'Lalb_Chr10g0095721' => 'lal', 'Lalb_Chr10g0095731' => 'lal', 'Lalb_Chr16g0387531' => 'lal', 'Lj1g0002269' => 'lja', 'Lj1g0014898' => 'lja', 'Lj2g0001507' => 'lja', 'Lj3A864G85' => 'lonja', 'Lj3C864T11' => 'lonja', 'Lj3g0020433' => 'lja', 'Lj3g0026893' => 'lja', 'Lj4g0000437' => 'lja', 'Lj4g0010019' => 'lja', 'Lj6C738G3' => 'lonja', 'Lj6g0015675' => 'lja', 'Lsat_1_v5_gn_3_53381' => 'lsa', 'Lsat_1_v5_gn_4_12500' => 'lsa', 'Lsat_1_v5_gn_6_95901' => 'lsa', 'Lsat_1_v5_gn_8_46261' => 'lsa', 'Lsat_1_v5_gn_8_46521' => 'lsa', 'Manes.15G134100' => 'mes', 'Manes.17G083800' => 'mes', 'Manes.17G083900' => 'mes', 'Mapoly0035s0137' => 'mpo', 'Mapoly0092s0044' => 'mpo', 'Mapoly0092s0046' => 'mpo', 'MBI13_g46817_MAGBIO' => 'mbi', 'MBI19_g37990_MAGBIO' => 'mbi', 'MCO03G394' => 'mco', 'MCO15G435' => 'mco', 'MD13G1020400' => 'mdo', 'MD13G1020500' => 'mdo', 'MD16G1018500' => 'mdo', 'MD16G1018600' => 'mdo', 'MD16G1018800' => 'mdo', 'MD16G1018900' => 'mdo', 'Medtr1g032110' => 'mtr', 'Medtr1g033440' => 'mtr', 'Medtr8g105270' => 'mtr', 'Medtr8g105290' => 'mtr', 'MELO3C026439.2' => 'cme', 'MELO3C026441.2' => 'cme', 'MELO3C034497.2' => 'cme', 'Migut.E00480' => 'egut', 'Migut.E00481' => 'egut', 'Migut.M00179' => 'egut', 'MSTRG.13626' => 'ama', 'MSTRG.2128' => 'ama', 'MSTRG.2129' => 'ama', 'MSTRG.7612' => 'ama', 'Nitab4.5_0000198g0160' => 'nta', 'Nitab4.5_0002134g0020' => 'nta', 'Nitab4.5_0002414g0110' => 'nta', 'Nitab4.5_0002803g0060' => 'nta', 'Nitab4.5_0004576g0040' => 'nta', 'Nitab4.5_0005073g0010' => 'nta', 'Nitab4.5_0005571g0010' => 'nta', 'Nitab4.5_0010421g0010' => 'nta', 'Nitab4.5_0026929g0010' => 'nta', 'Nn3g18359' => 'nnu', 'Nn4g24361' => 'nnu', 'Nn4g24372' => 'nnu', 'Oeu031609.1' => 'oeu', 'Oeu044011.1' => 'oeu', 'Oeu044012.1' => 'oeu', 'Oeu059515.2' => 'oeu', 'Oeu064208.1' => 'oeu', 'Os03g0223700' => 'osa', 'Os03g0223800' => 'osa', 'Os06g0305200' => 'osa', 'Peaxi162Scf00047g00710' => 'pax', 'Peaxi162Scf00337g00815' => 'pax', 'Peaxi162Scf00376g00816' => 'pax', 'Peaxi162Scf00376g00836' => 'pax', 'Peaxi162Scf01152g00010' => 'pax', 'Peaxi162Scf01152g00113' => 'pax', 'Peaxi162Scf01391g00116' => 'pax', 'PGR142G0042' => 'pgr', 'PGR142G2431' => 'pgr', 'PGSC0003DMG401029470' => 'stu', 'Phvul.002G321100' => 'pvu', 'Phvul.002G321200' => 'pvu', 'Phvul.003G019400' => 'pvu', 'Phvul.009G139600' => 'pvu', 'Potri.008G134600' => 'ptr', 'Potri.008G134800' => 'ptr', 'Potri.010G106700' => 'ptr', 'Pp3c11_22930' => 'ppa', 'Pp3c3_36400' => 'ppa', 'Pp3c3_36410' => 'ppa', 'Pp3c5_16790' => 'ppa', 'Pp3c6_9900' => 'ppa', 'Pp3c7_100' => 'ppa', 'Pp3c8_19610' => 'ppa', 'Pp3c8_3720' => 'ppa', 'PRCOL_00002290' => 'pco', 'PRCOL_00002396' => 'pco', 'Prupe.1G333200' => 'ppe', 'Prupe.1G333300' => 'ppe', 'Psat6g046320' => 'psa', 'Psat7g007960' => 'psa', 'Psat7g008000' => 'psa', 'Psat7g242680' => 'psa', 'PSO063G0325' => 'pso', 'PSO063G3102' => 'pso', 'PSO135G0439' => 'pso', 'PSO782G0639' => 'pso', 'PSO782G0822' => 'pso', 'QL02p058898' => 'qlo', 'QL02p059182' => 'qlo', 'QL03p035767' => 'qlo', 'QL03p035815' => 'qlo', 'RcHm_v2.0_Chr2g0167011' => 'rch', 'RcHm_v2.0_Chr2g0167021' => 'rch', 'RcHm_v2.0_Chr4g0443061' => 'rch', 'RcHm_v2.0_Chr4g0443071' => 'rch', 'Rhsim09G0089500' => 'rsi', 'Rhsim09G0089600' => 'rsi', 'Rhsim12G0118300' => 'rsi', 'Sabra08G0102800' => 'sbr', 'Sabra10G0077900' => 'sbr', 'SalBow2G2685' => 'sbo', 'SalBow2G3384' => 'sbo', 'Sc11g0004160' => 'sci', 'Sc11g0004180' => 'sci', 'Sc14g0006830' => 'sci', 'Sed0004382' => 'sed', 'Sed0007618' => 'sed', 'Sed0010499' => 'sed', 'Sed0013183' => 'sed', 'SEGI_06977' => 'sgi', 'SEGI_07920' => 'sgi', 'SEGI_09588' => 'sgi', 'SEGI_12334' => 'sgi', 'SEGI_12550' => 'sgi', 'SEGI_21189' => 'sgi', 'SGA_v2.0_scaffold151G36774' => 'sas', 'SGA_v2.0_scaffold23G10209' => 'sas', 'SGA_v2.0_scaffold23G10214' => 'sas', 'SHI04318' => 'shi', 'SMO134G0279' => 'smo', 'Solyc04g008010.4' => 'sly', 'Solyc05g017860.3' => 'sly', 'Solyc07g008160.3' => 'sly', 'Sopen04g003150' => 'spe', 'Sopen05g014620' => 'spe', 'Sopen07g004030' => 'spe', 'Sp1g13290' => 'spa', 'Sp2g13150' => 'spa', 'TAR371G0986' => 'tar', 'TAR622G0124' => 'tar', 'TAR629G0611' => 'tar', 'TAR629G0795' => 'tar', 'TAR629G1492' => 'tar', 'THA.LOC104805083' => 'tha', 'THA.LOC104823681' => 'tha', 'THA.LOC104824128' => 'tha', 'Thecc.02G292300' => 'tca', 'Thecc.02G292500' => 'tca', 'Thhalv10003708m.g' => 'esa', 'Thhalv10006562m.g' => 'esa', 'TPR.G15892' => 'tpr', 'TPR.G19247' => 'tpr', 'TPR.G19252' => 'tpr', 'TPR.G20324' => 'tpr', 'TPR.G36922' => 'tpr', 'TPR.G39980' => 'tpr', 'TWI53G1320' => 'twi', 'TWI74G0058' => 'twi', 'TWI74G0959' => 'twi', 'TWI77G0357' => 'twi', 'unitig_27.g25159' => 'ugi', 'unitig_27.g25160' => 'ugi', 'unitig_699.g19262' => 'ugi', 'unitig_85.g27249' => 'ugi', 'vmacro04889' => 'vma', 'vmacro09906' => 'vma', 'vmacro10692' => 'vma', 'vmacro10693' => 'vma', 'VMungo0251G0466' => 'vmu', 'VMungo0251G2427' => 'vmu', 'VMungo1215G0637' => 'vmu', 'Zm00001eb009100' => 'zma', 'Zm00001eb009110' => 'zma', 'Zm00001eb016220' => 'zma', 'Zm00001eb046330' => 'zma', 'Zm00001eb125500' => 'zma', 'Zm00001eb171960' => 'zma', 'Zm00001eb201400' => 'zma', 'Zm00001eb211590' => 'zma', 'Zm00001eb223660' => 'zma', 'Zm00001eb235300' => 'zma', 'Zm00001eb255180' => 'zma', 'Zm00001eb334690' => 'zma', 'Zm00001eb399840' => 'zma', 'Zm00001eb399850' => 'zma', 'Zm00001eb407740' => 'zma' ) $gf_id = 'HOM05D001486' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001486' ) $data_identifier = 'HOM05D001486' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 5, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 10, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 10, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 8, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407740' $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